Hello FreeSurfer group,
I am unable to run asegstats2table and cannot view asegstats2table --help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant.
When I use the following:
asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/
asegstats2table", line 4, in ? import os; ImportError: No module named os
Thank you for your time,
Jesse (Linux-centos4-stable-pub-v4.2.0)
On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe bledsoej@msu.edu wrote:
Hello,
I am having difficulty generating an aseg_stats.txt table.
When I use the following:
asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os
I am on Linux-centos4-stable-pub-v4.2.0
Any suggestions are much appreciated, Jesse
Hi Jesse
It seems there's something wrong with your Python installation.
Can you do the following?
type
python
and in the interpreter, enter
import os
and see if it works.
-Krish
On Dec 4, 2010, at 6:48 PM, Jesse Bledsoe wrote:
Hello FreeSurfer group,
I am unable to run asegstats2table and cannot view asegstats2table -- help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume -- tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os Thank you for your time,
Jesse (Linux-centos4-stable-pub-v4.2.0)
On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe bledsoej@msu.edu wrote: Hello,
I am having difficulty generating an aseg_stats.txt table.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume -- tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os
I am on Linux-centos4-stable-pub-v4.2.0
Any suggestions are much appreciated, Jesse
-- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Krish,
Thank you for the reply. After typing "import os" into the interpreter I get the following:
Traceback (most recent call last): File "<stdin>", line1, in ? ImportError: No module named os
Any suggestions?
Jesse
On Mon, Dec 6, 2010 at 2:12 PM, Krish Subramaniam <krish@nmr.mgh.harvard.edu
wrote:
Hi Jesse
It seems there's something wrong with your Python installation.
Can you do the following?
type
python
and in the interpreter, enter
import os
and see if it works.
-Krish
On Dec 4, 2010, at 6:48 PM, Jesse Bledsoe wrote:
Hello FreeSurfer group,
I am unable to run asegstats2table and cannot view asegstats2table --help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume --tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os Thank you for your time,
Jesse (Linux-centos4-stable-pub-v4.2.0)
On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe bledsoej@msu.edu wrote: Hello,
I am having difficulty generating an aseg_stats.txt table.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume --tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os
I am on Linux-centos4-stable-pub-v4.2.0
Any suggestions are much appreciated, Jesse
-- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jesse
it seems the standard Python is not installed with your CentOS installation. asegstats2table is a Python script and needs it.
You could either ask your sysadmin to install the Python. or if you have the permissions.. do it yourself -- some variant of
sudo yum install python
Best, Krish
On Dec 7, 2010, at 5:26 PM, Jesse Bledsoe wrote:
Hi Krish,
Thank you for the reply. After typing "import os" into the interpreter I get the following:
Traceback (most recent call last): File "<stdin>", line1, in ? ImportError: No module named os
Any suggestions?
Jesse
On Mon, Dec 6, 2010 at 2:12 PM, Krish Subramaniam <krish@nmr.mgh.harvard.edu
wrote:
Hi Jesse
It seems there's something wrong with your Python installation.
Can you do the following?
type
python
and in the interpreter, enter
import os
and see if it works.
-Krish
On Dec 4, 2010, at 6:48 PM, Jesse Bledsoe wrote:
Hello FreeSurfer group,
I am unable to run asegstats2table and cannot view asegstats2table -- help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume -- tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os Thank you for your time,
Jesse (Linux-centos4-stable-pub-v4.2.0)
On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe bledsoej@msu.edu wrote: Hello,
I am having difficulty generating an aseg_stats.txt table.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume -- tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os
I am on Linux-centos4-stable-pub-v4.2.0
Any suggestions are much appreciated, Jesse
-- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.
Hi Krish,
Thank you very much for your time, I will install the Python.
Jesse
On Wed, Dec 8, 2010 at 1:43 PM, Krish Subramaniam <krish@nmr.mgh.harvard.edu
wrote:
Hi Jesse
it seems the standard Python is not installed with your CentOS installation. asegstats2table is a Python script and needs it.
You could either ask your sysadmin to install the Python. or if you have the permissions.. do it yourself -- some variant of
sudo yum install python
Best, Krish
On Dec 7, 2010, at 5:26 PM, Jesse Bledsoe wrote:
Hi Krish,
Thank you for the reply. After typing "import os" into the interpreter I get the following:
Traceback (most recent call last): File "<stdin>", line1, in ? ImportError: No module named os
Any suggestions?
Jesse
On Mon, Dec 6, 2010 at 2:12 PM, Krish Subramaniam < krish@nmr.mgh.harvard.edu> wrote: Hi Jesse
It seems there's something wrong with your Python installation.
Can you do the following?
type
python
and in the interpreter, enter
import os
and see if it works.
-Krish
On Dec 4, 2010, at 6:48 PM, Jesse Bledsoe wrote:
Hello FreeSurfer group,
I am unable to run asegstats2table and cannot view asegstats2table --help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume --tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os Thank you for your time,
Jesse (Linux-centos4-stable-pub-v4.2.0)
On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe bledsoej@msu.edu wrote: Hello,
I am having difficulty generating an aseg_stats.txt table.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume --tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os
I am on Linux-centos4-stable-pub-v4.2.0
Any suggestions are much appreciated, Jesse
-- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.
Hi Krish,
Thank you very much. It turned out that program SureFit was causing problems with Python.
Just wanted to follow up in case others ran into the same problem,
Jesse
On Wed, Dec 8, 2010 at 1:43 PM, Krish Subramaniam <krish@nmr.mgh.harvard.edu
wrote:
Hi Jesse
it seems the standard Python is not installed with your CentOS installation. asegstats2table is a Python script and needs it.
You could either ask your sysadmin to install the Python. or if you have the permissions.. do it yourself -- some variant of
sudo yum install python
Best, Krish
On Dec 7, 2010, at 5:26 PM, Jesse Bledsoe wrote:
Hi Krish,
Thank you for the reply. After typing "import os" into the interpreter I get the following:
Traceback (most recent call last): File "<stdin>", line1, in ? ImportError: No module named os
Any suggestions?
Jesse
On Mon, Dec 6, 2010 at 2:12 PM, Krish Subramaniam < krish@nmr.mgh.harvard.edu> wrote: Hi Jesse
It seems there's something wrong with your Python installation.
Can you do the following?
type
python
and in the interpreter, enter
import os
and see if it works.
-Krish
On Dec 4, 2010, at 6:48 PM, Jesse Bledsoe wrote:
Hello FreeSurfer group,
I am unable to run asegstats2table and cannot view asegstats2table --help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume --tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os Thank you for your time,
Jesse (Linux-centos4-stable-pub-v4.2.0)
On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe bledsoej@msu.edu wrote: Hello,
I am having difficulty generating an aseg_stats.txt table.
When I use the following:
asegstats2table --subjects subject1 subject 2 --meas volume --tablefile aseg_stats.txt
I get the following error:
'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? import os; ImportError: No module named os
I am on Linux-centos4-stable-pub-v4.2.0
Any suggestions are much appreciated, Jesse
-- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________
Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.
freesurfer@nmr.mgh.harvard.edu
-
Jesse Bledsoe -
Krish Subramaniam